Liara, Tali, Garrus, and Kaiden/Ashely are the only ones I know will be back. Miranda will probably be back, since she turned on Cerberus and has no where else to go, as will most of your crew--but really, as long as Kelly's back, who cares about the rest? Anyway, here are my theories for why characters won't be joining again:
Grunt--He's formed his own clan under Wrex (who won't be back either). He's too busy helping the Krogan, but you can bet that when the showdown comes, he'll be helping in the final battle.
Kasumi--Either doing covert work for the Alliance, attempting to learn more about the Reapers, or she's dropped off the grid, like she said she was going to
Jacob--if he's not back like Miranda, then he's working Black Ops for the Alliance. After what he did, how could they not want him back?
Thane--Either dead, dying, or spending the remaining time of his life with his son. Personally, I think they're going to find a cure, but he's still going to be too weak to join the squad.
Jack--Jack is Jack. She'll either be on the team, or she'll be doing her own thing. I'm glad they decided to mellow her out a bit though. Looking forward to seeing her again.
Zaeed--if you didn't kill what's-his-name, Zaeed is tracking him down--which I hope he asks for my help, because I want him dead too, just not at the cost of innocents--but if you didn't, Zaeed is back in charge of the Blue Suns, attempting to fix their rep.
Legion--Legion probably will be returning because it was designed to follow Shep. If it's not back, then it has returned to Geth space in order to relay its findings, prepare for the attack, and attempt to make peace with The Creators (Quarians).
Morrdin--Attempting to find a cure for the Genophage, as his conscience finally caught up with him. Also, probably studying ways to combat Reaper tech.
Did I miss anyone? There were so many characters in the second game. What should be interesting is, what if one of these characters is your love interest. I can't imagine that person would not join your team--SAMARA!
Samara--Out doing Justicar work. She said that, after the mission was done, she still had work to do. She will always have work to do (her daughter will likely be out killing people if you chose her).
Anyway, back to what I was saying. Love interest should be rejoining your team, but how would that work? Jack, Thane, Jacob and Miranda are all love interest who are certain to return, so are they going to make different versions of your squad based on who you loved in the second game? Like Jack will only come back if she was your love interest, but otherwise she won't. Hm...
